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Population-scale genomics
As `struct` doesn't support properties that are not specified in the schema it errors out with a `KeyError` if `properties` is not present in the schema dict, for example `tskit.MetadataSchema({'codec':'struct'})`....
We are about to make a change to tsinfer so that the regions before the last site and after the last site in a tree sequence have no topology. I...
We will need to do this at some point, so opening issue to track.
Is this useful at all, or just an extra maintenance burden?
## Missingness added to forwards-backwards diploid LiS testing Added missingness, by including an emission probability of 1 for all missing characters in the query sequence.
When returning a node map from `simplify()`, I often find I need the inverted map (from new node ID to old), and have to remember every time the best way...
Some docstrings preface example code with `>>>`, e.g. https://tskit.dev/tskit/docs/stable/python-api.html#tskit.Tree.count_topologies and some don't, e.g. https://tskit.dev/tskit/docs/stable/python-api.html#tskit.Tree.prev I guess we should pick some convention (I think we could probably remove the `>>>`, so...
@savitakartik had an issue that she had an array of filenames of tree sequences, and was trying to load them using `tskit.load`. A bug in her script meant that some...
In #2823 we added support for the genetic_relatedness_matrix function as a follow-up usage of ``divergence_matrix`` using sample sets. This doesn't work when the sample_sets have a length > 1. It's...
## Description Add toy examples for testing imputation. Results obtained by running BEAGLE 4.1 are stored for comparison. Fixes #2802 # PR Checklist: - [x] Implement BEAGLE's interpolation-style imputation algorithm...
